Mercurial > repos > biowebdb > flowgram
changeset 1:dc29406ce984 draft
Uploaded
author | biowebdb |
---|---|
date | Mon, 31 Mar 2014 14:10:35 -0400 |
parents | d27bec235ad9 |
children | ce049751b625 |
files | sffextract.xml |
diffstat | 1 files changed, 75 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sffextract.xml Mon Mar 31 14:10:35 2014 -0400 @@ -0,0 +1,75 @@ +<tool id="biowebdb_flowgram_sffextract" name="sffextract" version="1.0.0"> + <description>Convert SFF to FastQ or Fasta/Qual</description> + <requirements> + <requirement type="binary">sff_extract</requirement> + </requirements> + <command interpreter="ruby">sffextract.rb + $input + #if str( $format_options.format ) == "FASTQ" + $output1 + #else + $output2 $output3 + #end if + </command> + <inputs> + <param name="input" type="data" format="sff" label="Input from 454 (flowgram - sff)" help="Only SFF file"/> + <conditional name="format_options"> + <param name="format" type="select" label="Output format" help=""> + <option value="FASTQ" selected="true">FastQ</option> + <option value="FASTA">Fasta</option> + </param> + </conditional> + </inputs> + <outputs> + <data name="output1" format="fastq" label="FASTQ - ${tool.name} on ${input.name}"> + <filter>format_options['format'] == 'FASTQ'</filter> + </data> + <data name="output2" format="fasta" label="FASTA - ${tool.name} on ${input.name}"> + <filter>format_options['format'] == 'FASTA'</filter> + </data> + <data name="output3" format="qual" label="QUAL - ${tool.name} on ${input.name}"> + <filter>format_options['format'] == 'FASTA'</filter> + </data> + </outputs> + <stdio> + <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> + <exit_code range="1:" level="fatal"/> + </stdio> + <tests> + <test> + <!-- + <param name="input" value="file454.sff"/> + <param name="format" value="FASTQ"/> + <output name="outfile1" file="file454.sff.fastq"/> + <output name="outfile1" file="file454.sff.fasta"/> + <output name="outfile2" file="file454.sff.qual"/> + --> + </test> + </tests> + <help> + +**If you use this tool, please cite:** + +| `Wagner G`_, Jardim R, Tschoeke DA, Loureiro DR, Ocana KACS, Ribeiro ACB, Emmel VE, +| Probst CM, Pitaluga AN, Grisard EC, Cavalcanti MC, Campos MLM, Mattoso M and `Dávila AMR`_ +| **STINGRAY: system for integrated genomic resources and analysis** +| BMC Research Notes 2014, 7:132 + +.. _Wagner G: glauber@ccb.ufsc.br +.. _Dávila AMR: davila@ioc.fiocruz.br + +----- + +If you have any questions or comments, feel free to `contact us`_. + +.. _contact us: jardim@ioc.fiocruz.br + +----- + +**Sff_extract information** + +454 sequence reads are usually stored in sff files. In these files the information about the reads is stored: sequece, quality and quality and adapter clips. sff_extract extracts the reads from the sff files and stores them into fasta and xml or caf text files. +sff_extract is a command line application written in python and it's free software distributed under the GPL licence. This software has been coded by Jose Blanca and Bastien Chevreux. See http://bioinf.comav.upv.es/sff_extract/index.html" + </help> + +</tool> \ No newline at end of file